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At the Krusty Krab, Squidward gives SpongeBob an order for a Krabby Patty. After making the patty, it begins to "move" and makes its way towards the front door. Mr. Krabs pulls Plankton off of the burger and sends him back to the Chum Bucket. Krabs explains that Plankton is his arch-competitor, and has been trying to steal the Krabby Patty's secret formula for years.
That night, after the Krusty Krab closes, Plankton tries to convince SpongeBob that they are friends, and that as such SpongeBob should give him a Krabby Patty. SpongeBob refuses and runs back home, but Plankton promises that SpongeBob will "hand deliver a Patty" to him.

Later that night, Plankton enters SpongeBob's head through a pore and makes his way to
SpongeBob's Brain. He attaches a mind control device to the brain and bends SpongeBob to his will, forcing him to walk to the Krusty Krab, get a Krabby Patty, and bring it to the Chum Bucket's Laboratory.
Plankton shows SpongeBob his computer, which can display the Ingredients of whatever he places in a nearby bowl. As a demonstration, he drops a piece of seaweed into the machine, to which Karen complies: 50% sea, 50% weed. Before he can force SpongeBob to drop the Krabby Patty in, SpongeBob begins a sorrowful ode to the Patty describing its tastiness. A hungry Plankton leaps onto the burger, bounces off its bun and falls into the bowl, and says "Oh Boy" before the computer displays his components (1% evil, 99% hot gas) on the computer screen. With Plankton stuck inside the computer, SpongeBob walks home.

This is the first appearance of Karen and Plankton, and also the second episode Doug Lawrence voiced in. The first was Ripped Pants.

SpongeBob's laugh is very different in this episode, as Tom Kenny was still trying to figure out how it should sound.

SpongeBob's line to Plankton when he is in his brain, "Leave my brain alone!", has become a staple on T-shirts and in pop culture for media manipulation.

When SpongeBob is walking towards his pants, the tie is red, but when the pants are just under his nose, it is black. This also happened in the episode Rock-A-Bye Bivalve.

Squidward's bedroom is on the first floor of his house instead of on the third floor.

In addition, this episode depicted Patrick's rock as hollow and that Patrick slept in the rock rather than under it.

Plankton changes sizes throughout the episode. When he is first seen, a magnifying glass is required to see him clearly. When he encountered SpongeBob, he's about the size of SpongeBob's finger. When he sneaks into SpongeBob's brain, he is about the size of a walnut. Then when he jumps to the Krabby Patty, he is the size of SpongeBob's finger again.

In this episode SpongeBob's mattress is full of flowers, but in other episodes his mattress is blank.

In this episode, SpongeBob's brain doesn't have a brain stem, but in episodes his brain stem is there.

When SpongeBob is asked for his "final words" (before he drops the patty) he reveals much of the recipe, but Plankton didn't notice.

According to the commentary on the Complete 1st Season DVD, there is a deleted scene in which Squidward is naked.